First, make sure your sublime-settings file is in the same directory as the corresponding tmPreferences file.
This is not true. You were probably mislead by the fact that you named the file incorrectly.
You can safely store you settings files inside Packages/User.
And to save yourself some head scratching on how to name the files and what settings are available check this:
1. Open file of the type you'd like to customize. Then go to Preferences -> Settings More -> Syntax Specific - User. Do your magic there and save, and surprisingly the file is in fact saved in Packages/User.
If you happen to have existing file for that language then it loads and you modify/save it.
2. Open command pallet and type "Preferences Default". Open the file and there lay all the settings for you to use.